Eukaryotic Systems Research Articles

The Eukaryotic System in the third update of the “Eukaryotic Supergroups: Taxonomy/Biotechnology Interface” (2024)

Updates of the eukaryotic system (domain Eukarya) in the interface “Eukaryotic supergroups: Taxonomy/Biotechnology interface” are described. The nine-kingdom system Eukarya has the following form: subdomain Excavata (kingdoms Archezoa, Discoba), subdomain Obimoda (kingdoms Crumalia, Amoebozoa, Obazoa), subdomain Corticata (kingdoms Eocorticata, Haptista, Tsaralia, Plantae incl. Cryptista, Glaucophyta, Rhodophyta, Chloroplastida).

Hyperglycosylation impairs the inhibitory activity of rCdtPLI2, the first recombinant beta-phospholipase A2 inhibitor

Crotoxin, a phospholipase A2 (PLA2) complex and the major Crotalus venom component, is responsible for the main symptoms described in crotalic snakebite envenomings and a key target for PLA2 inhibitors (PLIs). PLIs comprise the alpha, beta and gamma families, and, due to a lack of reports on beta-PLIs, this study aimed to heterologously express CdtPLI2 from Crotalus durissus terrificus venom gland to improve the knowledge of the neglected beta-PLI family. Thereby, recombinant CdtPLI2 (rCdtPLI2) was produced in the eukaryotic Pichia pastoris system to keep some native post-translational modifications. rCdtPLI2 (~41 kDa) presents both N- and O-linked glycans. Alpha-mannosidase digested-rCdtPLI2 (1 mol) strongly inhibited (73 %) CB-Cdc catalytic activity (5 mol), demonstrating that glycosylations performed by P. pastoris affect rCdtPLI2 action. Digested-rCdtPLI2 also inhibited PLA2s from diverse Brazilian snake venoms. Furthermore, rCdtPLI2 (1 mol) abolished the catalytic activity of Lmr-PLA2 (5 mol) and reduced the CTx-Cdc (5 mol) enzyme activity by 65 %, suppressing basic and acidic snake venom PLA2s. Additionally, crotalic antivenom did not recognize rCdtPLI2, suggesting a lack of neutralization by antivenom antibodies. These findings demonstrate that studying snake venom components may reveal interesting novel molecules to be studied in the snakebite treatment and help to understand these underexplored inhibitors.

A Lipase Gene of Thermomyces lanuginosus: Sequence Analysis and High-Efficiency Expression in Pichia pastoris.

Lipase, a type of enzyme that decomposes and synthesizes triglycerides, plays an important role in lipid processing. In this study, a heat-resisting lipase gene (lip4) from Thermomyces lanuginosus was subcloned into the pPICZαA vector and then transformed into Pichia pastoris X33. The recombinant yeast cell concentration reached the maximum (119.5 g/L) at 144 h, and the lipase (Lip4) activity reached the maximum (3900 U/mL) at 168 h in 10 L bioreactor. Through bioinformatics analysis, S168, as the key site of Lip4, participated in the formation of the catalytic triads S168-D223-H280 and G166-H167-S168-L169-G170. Furthermore, S168 and seven conserved amino acids of G104/288, S105, A195, P196, V225 and I287 constitute the active center of Lip4. Specifically, the structure modeling showed two α-helices of the lid domain, outside the active pocket domain, controlling the entry of the substrate on Lip4. The potential glycosylation of Asn-33 may be involved in exhibiting the high stable temperature for lipase activity. Therefore, the eukaryotic system was constructed to express Lip4 efficiently, and the amino acid sites related to the catalytic efficiency of Lip4 were clarified, providing a new way for its subsequent property research and industrial application.

Specialized contact sites regulate the fusion of chlamydial inclusion membranes

The intracellular bacterial pathogen Chlamydia trachomatis replicates within a membrane-bound compartment called the inclusion. Upon infection with several chlamydiae, each bacterium creates its own inclusion, resulting in multiple inclusions within each host cell. Ultimately, these inclusions fuse together in a process that requires the chlamydial protein IncA. Here, we show that inclusions form unique contact sites (inclusion contact sites, ICSs) prior to fusion, that serve as fusogenic platforms in which specific lipids and chlamydial proteins concentrate. Fusion depends on IncA clustering within ICSs and is regulated by PI(3,4)P2 and sphingolipids. As IncA concentrates within ICSs, its C-terminus likely interacts in trans with IncA on the apposing membrane, securing a high concentration of IncA at fusion sites. This regulatory mechanism contrasts with eukaryotic or viral fusion systems that are either composed of multiple proteins or use a change in pH to initiate membrane fusion. Thus, our study demonstrates that Chlamydia-mediated membrane fusion is primarily regulated by specific structural domains in IncA and its local organization on the inclusion membrane, which is affected by the host cell lipid composition.

Aescin Inhibits Herpes simplex Virus Type 1 Induced Membrane Fusion.

Infections with Herpes simplex virus can cause severe ocular diseases and encephalitis. The present study aimed to investigate potential inhibitors of fusion between HSV-1 and the cellular membrane of the host cell. Fusion and entry of HSV-1 into the host cell is mimicked by a virus-free eukaryotic cell culture system by co-expression of the HSV-1 glycoproteins gD, gH, gL, and gB in presence of a gD receptor, resulting in excessive membrane fusion and polykaryocyte formation. A microscopic read-out was used for the screening of potential inhibitors, whereas luminometric quantification of cell-cell fusion was used in a reporter fusion assay. HSV-1 gB was tagged at its C-terminus with mCherry to express mCherry-gB in both assay systems for the visualization of the polykaryocyte formation. Reporter protein expression of SEAP was regulated by a Tet-On 3 G system. The saponin mixture aescin was identified as the specific inhibitor (IC50 7.4 µM, CC50 24.3 µM, SI 3.3) of membrane fusion. A plaque reduction assay on Vero cells reduced HSV-1 entry into cells and HSV-1 cell-to-cell spread significantly; 15 µM aescin decreased relative plaque counts to 41%, and 10 µM aescin resulted in a residual plaque size of 11% (HSV-1 17 syn+) and 2% (HSV-1 ANG path). Release of the HSV-1 progeny virus was reduced by one log step in the presence of 15 µM aescin. Virus particle integrity was mainly unaffected. Analytical investigation of aescin by UHPLC-MS revealed aescin IA and -IB and isoaescin IA and -IB as the main compounds with different functional activities. Aescin IA had the lowest IC50, the highest CC50, and an SI of > 4.6.

Investigation and determination of CoQ10(H2) and CoQ10(H4) species from black yeast-like fungi and filamentous fungi.

Coenzyme Q (CoQ) or ubiquinone functions as an electron transporter in the electron transport system in both prokaryotes and eukaryotes. The isoprenyl side chain of CoQ is modified in some organisms, especially in fungi, for optimal electron transport performance under various conditions. In this study, we investigated the side chain saturated dihydro CoQ (CoQ10(H2)) in Aureobasidium pullulans EXF-150, Sydowia polyspora NBRC 30562, and naturally isolated Plowrightia sp. A37, all of which are melanized Dothideomycetes species within the Ascomycota, and also in filamentous fungi Aspergillus oryzae and Aspergillus terreus. Plowrightia sp. A37 produced the rarely synthesized tetrahydro type CoQ10(H4), especially in glucose-rich medium, during extended cultivation in contrast to CoQ10(H2) in time-limited cultivation. Using liquid chromatography-mass spectrometry, we identified demethoxyubiquinone-H2 (DMQ(H2)) as an indicative intermediate that suggests that the side chain-saturation of CoQ occurs after the formation of DMQ and not always in the last step as previously considered.

A bacterial immunity protein directly senses two disparate phage proteins.

Eukaryotic innate immune systems use pattern recognition receptors to sense infection by detecting pathogen-associated molecular patterns, which then triggers an immune response. Bacteria have similarly evolved immunity proteins that sense certain components of their viral predators, known as bacteriophages1-6. Although different immunity proteins can recognize different phage-encoded triggers, individual bacterial immunity proteins have been found to sense only a single trigger during infection, suggesting a one-to-one relationship between bacterial pattern recognition receptors and their ligands7-11. Here we demonstrate that the antiphage defence protein CapRelSJ46 in Escherichia coli can directly bind and sense two completely unrelated and structurally different proteins using the same sensory domain, with overlapping but distinct interfaces. Our results highlight the notable versatility of an immune sensory domain, which may be a common property of antiphage defence systems that enables them to keep pace with their rapidly evolving viral predators. We found that Bas11 phages harbour both trigger proteins that are sensed by CapRelSJ46 during infection, and we demonstrate that such phages can fully evade CapRelSJ46 defence only when both triggers are mutated. Our work shows how a bacterial immune system that senses more than one trigger can help prevent phages from easily escaping detection, and it may allow the detection of a broader range of phages. More generally, our findings illustrate unexpected multifactorial sensing by bacterial defence systems and complex coevolutionary relationships between them and their phage-encoded triggers.

Disentangling the Complexity in Protein Complexes Using Complementary Isotope-Labeling and Multiple-Receiver NMR Spectroscopy.

Intrinsically disordered proteins are abundant in eukaryotic systems, but they remain largely elusive pharmacological targets. NMR spectroscopy proved to be a suitable method to study these proteins and their interaction with one another or with drug candidates. Although NMR can give atomistic information about these interplays, molecular complexity due to severe spectral overlap, limited sample stability, and quantity remain an issue and hamper widespread applications. Here, we propose an approach to simultaneously map protein-protein binding sites onto two interacting partners by employing a complementary isotope-labeling strategy and a multiple receiver NMR detection scheme. With one partner being 15N,2H labeled and the interacting one being 13C,1H-labeled, we exploited proton and carbon detection to obtain clean and easily readable information. The method is illustrated with an application to the 50 kDa ternary protein complex formed between the prominent oncogenic transcription factor complex Myc/MAX and the tumor suppressor BRCA1.

A new Bowman-Birk type protease inhibitor regulated by MeJA pathway in maize exhibits anti-feedant activity against the Ostrinia furnacalis.

Jasmonic acid (JA), an important plant hormone, plays a crucial role in defending against herbivorous insects. In this study, we have identified a new Bowman-Birk type protease inhibitor (BBTI) protein in maize that is regulated by the JA pathway and exhibits significant antifeedant activity, which is notably induced by exogenous Methyl Jasmonate and Ostrinia furnacalis feeding treatments. Bioinformatics analysis revealed significant differences in the BBTI protein among different maize inbred lines, except for the conserved domain. Prokaryotic and eukaryotic expression systems were constructed and expressed, and combined with bioassays, it was demonstrated that the antifeedant activity of BBTI is determined by protein modifications and conserved domains. Through RT-qPCR detection of BBTI and JA regulatory pathway-related genes' temporal expression in different maize inbred lines, we identified the regulatory mechanism of BBTI synthesis under the JA pathway. This study successfully cloned and identified the MeJA-induced anti-feedant activity gene BBTI and conducted functional validation in different maize inbred lines, providing valuable insights into the response mechanism of insect resistance induced by the plant JA pathway. The increased expression of the anti-feedant activity gene BBTI through exogenous MeJA induction may offer a potential new strategy for mediating plant defense against Lepidoptan insects.

Получение и оценка биологической активности экзогенной мРНК, кодирующей белок MxA человека

Human MxA protein induced by type I and III interferons is an important innate immunity mediator, it shows antiviral activity against a broad spectrum of RNA and DNA viruses. According to the latest data, the MxA protein overexpression increases chemotherapy sensitivity and represents one of the favorable prognostic factors in patients with breast cancer. The exogenous mRNA capable of intracellular MxA protein production not only has the potential for treatment of viral respiratory infection, but also can become an important fundamental research tool. The study aimed to construct and produce the exogenous mRNA encoding the functional human cytoplasmic MxA protein by in vitro transcription (IVT); to study its translational properties; to assess and identify the patterns of the expression of some interferon system genes in response to introduction of this exogenous mRNA into cells. As a result of the study, the exogenous mRNAs capable of effective translation (up to 20 ng/mL of protein from 100 ng of mRNA per well of the 96-well plate) in the eukaryotic cell systems were successfully constructed and produced by IVT (in the amount of up to 200 µg); diffuse distribution of the MxA protein in the MDCK cells was confirmed; significant changes in the expression of the interferon-stimulated genes, such as OAS1, PKR (EIF2AK2), MDA5, RIG-I, were revealed. Our further research will be focused on assessing the developed exogenous mRNAs’ therapeutic potential against influenza A and B viruses, respiratory syncytial virus, and coronavirus SARS-CoV-2.

Identification of a novel conserved B-cell epitope in p15 of the African swine fever virus

African Swine Fever Virus (ASFV), a highly contagious DNA virus, causes severe economic losses to the global swine industry. The ASFV p15 protein, which is found in the core shell, is essential to the assembly of viral particles. In addition, protein p15 is a candidate target for the development of diagnostic reagents for African Swine Fever (ASF) because of its excellent immunogenicity. In this research, we prepared the p15 protein using eukaryotic expression system and validated it with sera from ASFV-infected pigs. The p15 protein could be well identified by the sera from ASFV-infected pigs, suggesting that some linear epitopes are located in the p15 protein. Furthermore, we successfully prepared two lgG1 subclass monoclonal antibodies (1E6-A7 and 3D7C9) specific against p15 using hybridoma technology. Using the peptide scanning method, we discovered the two mAbs well recognized the same linear epitope23LEIINNLCML32. The23LEIINNLCML32 epitope in the ASFV p15 N-terminus was identified and characterized for the first time, and it reacted well with the ASFV-positive serum, implying that it was a natural B cell linear epitope. These findings may help in the development of novel serologic diagnosis tools and the improvement of antiviral drug designs for ASF.

Engineered IgG Fc-conjugation prolongs the half-life of florfenicol and alleviates pneumonia in mice

Small molecule drugs often exhibit short half-lives, requiring frequent administrations to maintain therapeutic concentrations over an extended period. To address this issue, the fragment crystallizable (Fc) region of IgG, known to prolong the half-life of antibodies via its interaction with the Fc neonatal receptor, was harnessed as a carrier protein to extend the half-life of a small molecule drug, florfenicol. Florfenicol, was chemically coupled to a recombinant Fc protein expressed using the eukaryotic expression system in HEK293 cells. The Fc-florfenicol conjugate exhibited a substantially prolonged half-life of from 3.8 to 9.1 hours compared to unconjugated florfenicol and demonstrated excellent therapeutic properties in treating pneumonia in a mouse model. Our results, combined with the literature analysis on Fc-small molecule conjugates, show that Fc can substantially enhance the drug’s half-life and suggest the potential for its use as a carrier in novel delivery systems.

Directed evolution of an orthogonal transcription engine for programmable gene expression in eukaryotes.

T7 RNA polymerase has enabled orthogonal control of gene expression and recombinant protein production across diverse prokaryotic host chassis organisms for decades. However, the absence of 5' methyl guanosine caps on T7 RNAP derived transcripts has severely limited its utility and widespread adoption in eukaryotic systems. To address this shortcoming, we evolved a fusion enzyme combining T7 RNAP with the single subunit capping enzyme from African swine fever virus using Saccharomyces cerevisiae. We isolated highly active variants of this fusion enzyme, which exhibited roughly two orders of magnitude higher protein expression compared to the wild-type enzyme. We demonstrate the programmable control of gene expression using T7 RNAP-based genetic circuits in yeast and validate enhanced performance of these engineered variants in mammalian cells. This study presents a robust, orthogonal gene regulatory system applicable across diverse eukaryotic hosts, enhancing the versatility and efficiency of synthetic biology applications.

Dimerization Promotes PKR Activation by Modulating Energetics of αC Helix Conversion between Active and Inactive Conformations.

Protein kinase R (PKR) functions in the eukaryotic innate immune system as a first-line defense against viral infections. PKR binds viral dsRNA, leading to autophosphorylation and activation. In its active state, PKR can phosphorylate its primary substrate, eIF2α, which blocks the initiation of translation in the infected cell. It has been established that PKR activation occurs when the kinase domain dimerizes in a back-to-back configuration. However, the mechanism by which dimerization leads to enzymatic activation is not fully understood. Here, we investigate the structural mechanistic basis and energy landscape for PKR activation, with a focus on the αC helix─a kinase activation and signal integration hub─using all-atom equilibrium and enhanced sampling molecular dynamics simulations. By employing window-exchange umbrella sampling, we compute free-energy profiles of activation, which show that back-to-back dimerization stabilizes a catalytically competent conformation of PKR. Key hydrophobic residues in the homodimer interface contribute to stabilization of the αC helix in an active conformation and the position of its critical glutamate residue. Using linear mutual information analysis, we analyze allosteric communication connecting the protomers' N-lobes and the αC helix dimer interface with the αC helix.

A functional screen for ubiquitin regulation identifies an E3 ligase secreted by Pseudomonas aeruginosa.

Ubiquitin signaling controls many aspects of eukaryotic biology, including targeted protein degradation and immune defense. Remarkably, invading bacterial pathogens have adapted secreted effector proteins that hijack host ubiquitination to gain control over host responses. These ubiquitin-targeted effectors can exhibit, for example, E3 ligase or deubiquitinase activities, often without any sequence or structural homology to eukaryotic ubiquitin regulators. Such convergence in function poses a challenge to the discovery of additional bacterial virulence factors that target ubiquitin. To overcome this, we have developed a workflow to harvest natively secreted bacterial effectors and functionally screen them for ubiquitin regulatory activities. After benchmarking this approach on diverse ligase and deubiquitinase activities from Salmonella Typhimurium, Enteropathogenic Escherichia coli, and Shigella flexneri, we applied it to the identification of a cryptic E3 ligase activity secreted by Pseudomonas aeruginosa. We identified an unreported P. aeruginosa E3 ligase, which we have termed Pseudomonas Ub ligase 1 (PUL-1), that resembles none of the other E3 ligases previously established in or outside of the eukaryotic system. Importantly, in an animal model of P. aeruginosa infection, PUL-1 ligase activity plays an important role in regulating virulence. Thus, our workflow for the functional identification of ubiquitin-targeted effector proteins carries promise for expanding our appreciation of how host ubiquitin regulation contributes to bacterial pathogenesis.

Production Technologies for Recombinant Antibodies: Insights into Eukaryotic, Prokaryotic, and Transgenic Expression Systems.

Recombinant antibodies, a prominent class of recombinant proteins, are witnessing substantial growth in research and diagnostics. Recombinant antibodies are being produced employing diverse hosts ranging from highly complex eukaryotes, for instance, mammalian cell lines (and insects, fungi, yeast, etc.) to unicellular prokaryotic models like gram-positive and gram-negative bacteria. This review delves into these production methods, highlighting approaches like antibody phage display that employs bacteriophages for gene library creation. Recent studies emphasize monoclonal antibody generation through hybridoma technology, utilizing hybridoma cells from myeloma and B-lymphocytes. Transgenic plants and animals have emerged as sources for polyclonal and monoclonal antibodies, with transgenic animals preferred due to their human-like post-translational modifications and reduced immunogenicity risk. Chloroplast expression offers environmental safety by preventing transgene contamination in pollen. Diverse production technologies, such as stable cell pools and clonal cell lines, are available, followed by purification via techniques like affinity chromatography. The burgeoning applications of recombinant antibodies in medicine have led to their large-scale industrial production.

The Prokaryotic Roots of Eukaryotic Immune Systems.

Over the past two decades, studies have revealed profound evolutionary connections between prokaryotic and eukaryotic immune systems, challenging the notion of their unrelatedness. Immune systems across the tree of life share an operational framework, shaping their biochemical logic and evolutionary trajectories. The diversification of immune genes in the prokaryotic superkingdoms, followed by lateral transfer to eukaryotes, was central to the emergence of innate immunity in the latter. These include protein domains related to nucleotide second messenger-dependent systems, NAD+/nucleotide degradation, and P-loop NTPase domains of the STAND and GTPase clades playing pivotal roles in eukaryotic immunity and inflammation. Moreover, several domains orchestrating programmed cell death, ultimately of prokaryotic provenance, suggest an intimate link between immunity and the emergence of multicellularity in eukaryotes such as animals. While eukaryotes directly adopted some proteins from bacterial immune systems, they repurposed others for new immune functions from bacterial interorganismal conflict systems. These emerging immune components hold substantial biotechnological potential.

Generating Cytokines and Growth Factors for Functional Activity: Feasibility of Method Using MIF Protein.

Cytokines and growth factors are signaling molecules that regulate a variety of biological processes. Understanding their role is essential for basic research and clinical utilization. Thus, cytokines and growth factors are widely used throughout research labs in a significant number of applications. Additionally, genetic polymorphisms result in variant forms of cytokines and growth factors, which can alter their function. Becoming more common, researchers will need to generate these important proteins and their variants themselves in functional forms for activity studies. The expression systems used to generate these proteins can have a major impact on their function. In some instances, post-translational modifications are needed to produce a functionally active protein, which can only be conducted using eukaryotic expression systems. Ideally, for functional relevance, a human expression system should be used for human-related research and applications. Most human cell-based expression systems primarily use HEK (Human Embryonic Kidney) cells; however, relying on just one cell type can lead to several issues, considering the variety of proteins derived from various cell sources. Here, we provide a protocol to effectively and efficiently generate functional recombinant proteins, taking into consideration the diverse range of proteins from different cell types throughout the human body.

Cloning and expression of UbiA human gene using innovative methodologies for recombinant protein production in PUAST vector

Introduction: A systematic library of Gal4/UAS-regulated transgenes has proven to be a powerful genetic system for identifying genes and defining pathways in development. This system offers valuable insights that highlight the evolutionary conservation between animals and humans. Objectives: The objective of this study was to clone, express, and characterize the UbiA gene. The research presents a highly effective method for cloning genes, using the UbiA-pcDNA3 gene as a model for mammalian cloning. These genes were then integrated into the PUAST vector of Drosophila, an expression vector and eukaryotic cell system commonly used for producing recombinant proteins. Materials and Methods: UbiA was isolated from human cells, and complementary DNA was synthesized. An oligonucleotide primer pair was designed based on the UbiA gene sequence, incorporating XhoI and Xbal restriction sites at the 5´ end of the forward and reverse primers, respectively. The UbiA gene was then amplified by PCR, cloned into the pcDNA3 plasmid, and the resulting recombinant plasmid was sequenced. Subsequently, the gene was sub cloned into the PUAST vector and expressed in S2 cells as a eukaryotic cell system. Protein determination and verification were conducted through western blotting techniques. Results: Confirmation of UbiA gene cloning into the PUAST vector was achieved through colony-PCR and digestion by enzymes. Cloning and sub cloning techniques validated by enzymatic digestion, along with gene sequencing. The identity between cloned UbiA gene and the identical gene exhibited 99%. We revealed a singular band purified protein through western blotting with 60 kDa size. Conclusion: More protein synthesis of the UbiA gene can be achieved by using the eukaryotic expression system provided by the PUAST vector. This technique has been proven to be a suitable platform and can be instrumental in various applications such as therapeutics, pharmacology, and vaccine development.

Single-Molecule Studies of Cognate and Near-Cognate Elongation in an in vitro Eukaryotic Translation System.

The ribosome plays a central role in translation of the genetic code into amino acid sequences during synthesis of polypeptides. During each cycle of peptide elongation, the ribosome must discriminate between correct and incorrect aminoacyl-tRNAs according to the codon present in its A-site. Ribosomes rely on a complex sequence of proofreading mechanisms to minimize erroneous selection of incorrect aminoacyl-tRNAs that would lead to mistakes in translation. These mechanisms have been studied extensively in prokaryotic organisms, but eukaryotic elongation is less well understood. Here, we use single-molecule fluorescence resonance energy transfer (smFRET) with an in vitro eukaryotic translation system to investigate tRNA selection and subsequent steps during peptide elongation. We compared accommodation of a tryptophan-aminoacyl-tRNA into the ribosomal A-site containing either a cognate or near-cognate codon and unexpectedly found that, following an initial slow sampling event, subsequent near-cognate sampling events proceeded more rapidly than the initial event. Further, we found a strong negative correlation between the concentration of near-cognate aminoacyl-tRNA and the efficiency of tRNA accommodation. These novel characteristics of near-cognate interaction with the eukaryotic ribosome suggest that rejection of a near-cognate tRNAs leads to formation of an altered ribosomal conformation that assists in rejecting subsequent incorrect tRNA interactions.